rs4771996

chr13-97401538-G-Achr13-97401538-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.828 in 152,096 control chromosomes in the GnomAD database, including 52,470 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.83 (52470 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125852 AN: 151976 Hom.: 52415 Cov.: 31

Gnomad AFR AF: 0.904

Gnomad AMI AF: 0.895

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.843

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.828 AC: 125962 AN: 152096 Hom.: 52470 Cov.: 31 AF XY: 0.825 AC XY: 61329 AN XY: 74342

Gnomad4 AFR AF: 0.904

Gnomad4 AMR AF: 0.803

Gnomad4 ASJ AF: 0.914

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.712

Gnomad4 NFE AF: 0.803

Gnomad4 OTH AF: 0.843

Alfa AF: 0.823 Hom.: 51488

Bravo AF: 0.838

Asia WGS AF: 0.770 AC: 2679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.2
Dann	Benign	0.30

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4771996; hg19: chr13-98053792;